I would say that most merchant ships had minimal colors used on them because colored paint was expensive and not something they would want to spend money on. Most would probably have been painted black with perhaps some white or tallow in the paint scheme, especially the lower hull. I doubt that stains were in use at that time. If you do a search in Google for "merchant ships 1700 images," you'll see photos of replica's and drawings of some merchant ships to get an idea of the colors used. It might also depend on the country of the ship as well.
Here is the ANCRE colour chart for 18th century French ships. Note the softer warmer tones quite unlike the bright colder synthetic modern colours. Though these are French applicable there would have been some cross over with colours for other European countries as paint technology was very similar. Research is required to how and where they were used.